Commonly, one of the challenges in the development of today’s nanodevices is the integration of nano-objects or molecules onto desired locations on a substrate. This integration comprises their accurate positioning, their alignment and the preservation of their functionality with respect to assembly processes. Required are novel engineering approaches to overcome this problem. Here, we prove how capillary assembly in combination with soft-lithography can be used to perform phage lambda DNA molecular combing to generate chips of isolated DNA strands for genetic analysis and diagnosis. The assembly of DNA molecules was achieved on a topologically micropatterned polydimethylsiloxane (PDMS) stamp inducing almost simultaneously the trapping and stretching of single molecules. The DNA molecules were then transfer printed onto a glass slide coated by vapour deposition of 3-aminopropyltrimethoxysilane (APTMS) molecules. In fact, this technique offers the possibility to tightly control the experimental parameters to direct the assembly process in a highly reproducible manner. We can easily create arrays or more complex networks of stretched DNA molecules with high yield, while preserving their functionality.